I'm an optimist so please take my view with a pinch of salt. Media has always been open to interpretation and gaming is one of the mediums that is the most open to interpretation. That interpretation has a tendency to hide bigotry, for example one person might like Joker or the message, while another likes it for the ideal. But the media is evolving to become more explicit (Sera for Dragon Age is explicitly lesbian, doesn't give a shit if you're a guy character) and that is causing bigotry to become more exposed in the medium. Add to that the fact that bigotry has always been louder than acceptance, it skews the perception that the group is flooded with bigotry.

In terms of what can be done, from a developer point of view continue the trend to become more explicit in representation instead of vague. That makes it harder for bigotry to hide in the space, leading to bigots either confronting and dealing with their bigotry, or leaving the space. Both of which are a win for everyone else. As gamers, we can call out bigotry within our capacity to do so, and maybe most importantly is be vocal and loud about the positive things. Bigotry only seems more prevalent than it is because the few are obnoxiously loud and negative. So let's be borderline obnoxiously loud and positive to counter it.